What I would advise, is have everything in one big
/ partition on the SSD (including your home directories), and then, if the SSD is not big enough for all your large files, mount your HDD separately as, say,
/media/BigHDD or whatever, and put your large files there.
That way, all your dotfiles (files and directories beginning with a dot in your home directory) will be on the SSD, including new ones that software might create. It is often these dotfiles (particularly
.cache) that are frequently read and written to and therefore would benefit from SSD the most. But that isn't to say other files and directories wouldn't also benefit.
If your SSD space is not particularly limited, there is no reason to keep anything off of it. Have everything on it. Then, if you need to store lots of large files, such as for video editing, photography, your music collection, etc and these don't fit on there, then have a separately mounted drive for these.
I used to use an Asus EeePC 900. That thing had a 4GB primary SSD. That is limited space, requiring careful partitioning. A 40GB SSD is not limited.
If I had to write a list of what things would most benefit from being on an SSD I'd put them in this order.
~/.cache - the cache area of your home directory, where software like browsers keep their cache.
/lib - just to improve start-up time of applications, and boot time.
/etc - some software needs to read a lot of files in here when it starts.
/tmp - some software uses this for temporary storage, but less so for user software.
/var - system software sometimes stores temporary or frequently changing files here.
~/.config - config files for your user software and account.
As you can see, it's somewhat spread out over the drive.
It may be more useful to see a list of what doesn't benefit so much from being on an SSD:
Media files, like music and videos.
Any other large documents, like the original images if you do photography.
Backups or large archives (eg, of other systems)